autoplot.R
In ggcyto: Visualize Cytometry data with ggplot

## ---- echo=FALSE--------------------------------------------------------------
knitr::opts_chunk$set(message = FALSE, warning = FALSE)

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library(ggcyto)
dataDir <- system.file("extdata",package="flowWorkspaceData")
gs <- load_gs(list.files(dataDir, pattern = "gs_bcell_auto",full = TRUE))
data(GvHD)
fs <- GvHD[subset(pData(GvHD), Patient %in%5 & Visit %in% c(5:6))[["name"]]]

## -----------------------------------------------------------------------------
autoplot(fs, x = 'FSC-H')

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autoplot(fs, x = 'FSC-H', y = 'SSC-H', bins = 64)

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autoplot(fs[[1]]) + labs_cyto("marker")

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autoplot(gs, "CD3", bins = 64)

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autoplot(gs, c("CD3", "CD19"), bins = 64)

## ---- fig.width = 4, fig.height=3---------------------------------------------
gh <- gs[[1]]
nodes <- gs_get_pop_paths(gh, path = "auto")[c(3:6)]
nodes

autoplot(gh, nodes, bins = 64)

## ---- fig.width = 8, fig.height=3---------------------------------------------
# get ggcyto_GatingLayout object from first sample
res <- autoplot(gs[[1]], nodes, bins = 64)
class(res)
# arrange it as one-row gtable object 
gt <- ggcyto_arrange(res, nrow = 1)
gt
# do the same to the second sample
gt2 <- ggcyto_arrange(autoplot(gs[[2]], nodes, bins = 64), nrow = 1)
# combine the two and print it on the sampe page
gt3 <- gridExtra::gtable_rbind(gt, gt2)
plot(gt3)